02-251 Great Ideas in Computational Biology

Spring 2019
Date Lecture Topic Instructor
1/15 Introduction
Genome assembly (Part 1)
1/17 Genome assembly (Complete) Compeau
1/18 Recitation on Genome Assembly TAs
1/22 Sequence alignment (Part 1)
Alignment Demo
1/24 Sequence alignment (Part 2) Kingsford
1/25 Recitation on Dynamic Programming TAs
1/29 Read mapping (Part 1)
Suffix Tree Math
1/31 No Class (cancelled due to cold) Polar Vortex
2/1 Recitation on Read Mapping (Part 1) TAs
2/5 Read mapping (Part 2) Compeau
2/7 Multiple sequence alignment Kingsford
2/8 Recitation on Read Mapping (Part 2) TAs
2/12 Mini-lecture day 1
2/14 Midterm 1
2/19 Hidden Markov models Kingsford
2/21 Metagenomics Compeau
2/22 Recitation on HMMs TAs
2/26 Phylogenetics (in progress) Compeau
2/28 Phylogenetics (complete) and some necessary mathematics Compeau
3/1 MCMC for Phylogenetics TAs
3/5 Motif Finding, Gibbs Sampling, EM Kingsford
3/7 RNA sequencing, gene expression Kingsford
S P R I N G   B R E A K
3/19 Network biology: intro & function prediction Kingsford
3/21 Network biology: evolution of modularity Kingsford
3/26 Population Genetics Compeau
3/28 Mini-lecture day 2
3/29 Recitation on Soft Clustering TAs
4/2 Midterm 2
Note: All topics after Midterm 2 are tentative and subject to change.
4/4 Evolutionary Game Theory
Animated GIF
4/9 Neural Modeling Kingsford
S P R I N G   C A R N I V A L
4/16 Universality of Neural Networks and Deep Learning (incomplete) Compeau
4/18 Protein Structure Prediction Kingsford
4/19 Recitation on Neural Nets TAs
4/23 Finishing up Neural Nets Compeau
4/25 Three Mini-"Great Ideas": Turing Patterns, Fragile Genomes, and DNA Computing Compeau
4/26 Drop-in Project Office Hours During Recitation TAs
4/30 Project Presentations Students
5/2 Project Presentations Students